Immune profiling of COVID-19-infected patients admitted to the Intensive Care Unit (ICU) - Fluidigm - qRT-PCR - 96 Gene Panel
- 1. Data and associated plots based on the Ct values
- 1.1 Sample metadata - Data table
- 1.2 Ct value - Data table
- 1.3 Housekeeping Genes Ct value - Data table
- 1.4 Box Plot - Ct values of Housekeeping Genes based on ‘sample plate effect’
- 1.5 Box Plot - Ct values of all samples based on ‘sample plate effect’
- 1.6 Density Plot - Ct values of all samples’
- 1.7 Density Plot - Ct values of all samples based on ‘sample plate effect’ - color fill
- 1.8 Density Plot - Ct values of all samples’ based on ‘sample plate effect’ - semi-transparent fill
- 1.9 Scree Plot to determine No. of PCs - Ct values of all samples
- 1.10 PCA Plot - Ct values of all samples based on ‘sample plate effect + type’
- 1.11 PCA Plot - Ct values of all samples based on ‘type + timepoints’
- 1.12 PCA Plot with ellipse - Ct values of all samples based on ‘type + timepoints’
- 1.13 PCA Plot with ellipse - Ct values of all samples based on ‘timepoints + type’
- 2. Data and associated plots based on the Negative Delta Ct values [log normalized]
- 2.1 Delta Ct value - Data table
- 2.2 Negative Delta Ct value [log normalized] - Data table
- 2.3 Box Plot - Negative Delta Ct values [log normalized] of all samples based on ‘sample plate effect’
- 2.4 Density Plot - Negative DCt Values [log normalized] of all samples’
- 2.5 Density Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect’ - color fill
- 2.6 Density Plot - Negative Delta Ct Values [log normalized] of all samples’ based on ‘sample plate effect’ - semi-transparent fill
- 2.7 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] of all samples
- 2.8 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect + type’
- 2.9 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’
- 2.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’
- 2.11 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘timepoints + type’
- 2.12 Delta Delta Ct (Covid-19 vs. Healthy Control) - Data table
- 2.13 Fold Change - Linear (Covid-19 vs. Healthy Control) - Data table
- 2.14 Fold Change - Inverse Scale (Covid-19 vs. Healthy Control) - Data table
- 2.15 Fold Change - Log Scale (Covid-19 vs. Healthy Control) - Data table
- 2.16 Delta Delta Ct [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.17 Fold Change - Linear [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.18 Fold Change - Inverse Scale [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.19 Fold Change - Log Scale [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.20 Statistical Analysis from limma on Negative Delta Ct (log normalized)- between Covid-19 vs. Healthy Control - Data table
- 2.21 Venn Diagram - between Covid-19 vs. Healthy Control - Data table
- 2.22 Statistical Analysis from limma on Negative Delta Ct (log normalized)- between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.23 Venn Diagram from limma - between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 3. Data and associated plots based on the Negative Delta Ct values [log normalized] - Batch Corrected (ComBat function from SVA- R Package)
- 3.1 Negative Delta Ct value [log normalized] - Batch Corrected - Data table
- 3.2 Box Plot - Negative Delta Ct values [log normalized] - Batch Correction of all samples based on ‘sample plate effect’
- 3.3 Density Plot - Negative DCt Values [log normalized] - Batch Correction of all samples’
- 3.4 Density Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘sample plate effect’ - color fill
- 3.5 Density Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples’ based on ‘sample plate effect’ - semi-transparent fill
- 3.6 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] - Batch Correction of all samples
- 3.7 PCA Plot - Negative Delta Ct Values [log normalized] - Batch Correction of of all samples based on ‘sample plate effect + type’
- 3.8 PCA Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘type + timepoints’
- 3.9 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘type + timepoints’
- 3.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘timepoints + type’
1. Data and associated plots based on the Ct values
1.1 Sample metadata - Data table
Download Sample_metadata.csv1.2 Ct value - Data table
Download Ct values.csv1.3 Housekeeping Genes Ct value - Data table
Download Housekeeping Genes Ct values.csv1.4 Box Plot - Ct values of Housekeeping Genes based on ‘sample plate effect’
1.5 Box Plot - Ct values of all samples based on ‘sample plate effect’
1.6 Density Plot - Ct values of all samples’
1.7 Density Plot - Ct values of all samples based on ‘sample plate effect’ - color fill
1.8 Density Plot - Ct values of all samples’ based on ‘sample plate effect’ - semi-transparent fill
1.9 Scree Plot to determine No. of PCs - Ct values of all samples
1.10 PCA Plot - Ct values of all samples based on ‘sample plate effect + type’
1.11 PCA Plot - Ct values of all samples based on ‘type + timepoints’
1.12 PCA Plot with ellipse - Ct values of all samples based on ‘type + timepoints’
1.13 PCA Plot with ellipse - Ct values of all samples based on ‘timepoints + type’
2. Data and associated plots based on the Negative Delta Ct values [log normalized]
2.1 Delta Ct value - Data table
Download Delta Ct.csv2.2 Negative Delta Ct value [log normalized] - Data table
Download Negative Delta Ct.csv2.3 Box Plot - Negative Delta Ct values [log normalized] of all samples based on ‘sample plate effect’
2.4 Density Plot - Negative DCt Values [log normalized] of all samples’
2.5 Density Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect’ - color fill
2.6 Density Plot - Negative Delta Ct Values [log normalized] of all samples’ based on ‘sample plate effect’ - semi-transparent fill
2.7 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] of all samples
2.8 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect + type’
2.9 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’
2.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’
2.11 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘timepoints + type’
2.12 Delta Delta Ct (Covid-19 vs. Healthy Control) - Data table
Download DDCt Covid19 vs Healthy Control.csv2.13 Fold Change - Linear (Covid-19 vs. Healthy Control) - Data table
Download Fold Change Linear Covid19 vs Healthy Control.csv2.14 Fold Change - Inverse Scale (Covid-19 vs. Healthy Control) - Data table
Download Fold Change Linear Inverse Covid19 vs Healthy Control.csv2.15 Fold Change - Log Scale (Covid-19 vs. Healthy Control) - Data table
Download Fold Change Log Covid19 vs Healthy Control.csv2.16 Delta Delta Ct [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
Download DDCt Covid19 Timepoints (TP 1-4) vs Healthy Control (TP1).csv2.17 Fold Change - Linear [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
Download Fold Change Linear Covid19 Timepoints (TP 1-4) vs Healthy Control (TP1).csv2.18 Fold Change - Inverse Scale [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
Download Fold Change Linear Inverse Covid19 Timepoints (TP 1-4) vs Healthy Control (TP1).csv2.19 Fold Change - Log Scale [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
Download Fold Change Log Covid19 Timepoints (TP 1-4) vs Healthy Control (TP1).csv2.20 Statistical Analysis from limma on Negative Delta Ct (log normalized)- between Covid-19 vs. Healthy Control - Data table
Download Statistical Analysis Covid19 vs Healthy Control.csv2.21 Venn Diagram - between Covid-19 vs. Healthy Control - Data table
2.22 Statistical Analysis from limma on Negative Delta Ct (log normalized)- between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
Download Statistical Analysis [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)].csv2.23 Venn Diagram from limma - between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
3. Data and associated plots based on the Negative Delta Ct values [log normalized] - Batch Corrected (ComBat function from SVA- R Package)
3.1 Negative Delta Ct value [log normalized] - Batch Corrected - Data table
Download Negative Delta Ct Batch Corrected.csv3.2 Box Plot - Negative Delta Ct values [log normalized] - Batch Correction of all samples based on ‘sample plate effect’
3.3 Density Plot - Negative DCt Values [log normalized] - Batch Correction of all samples’
3.4 Density Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘sample plate effect’ - color fill
3.5 Density Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples’ based on ‘sample plate effect’ - semi-transparent fill
3.6 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] - Batch Correction of all samples
3.7 PCA Plot - Negative Delta Ct Values [log normalized] - Batch Correction of of all samples based on ‘sample plate effect + type’
3.8 PCA Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘type + timepoints’
3.9 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘type + timepoints’
3.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘timepoints + type’
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